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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/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' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ), 'gf_id' => 'HOM05D001240', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001240' ), 'data_identifier' => 'HOM05D001240', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001240', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '503', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p33570' => 'bna', 'A04p33580' => 'bna', 'A05p05070' => 'bna', 'A05p05080' => 'bna', 'A08p00780' => 'bna', 'Aa31LG10G1020' => 'aar', 'Aa31LG1G26550' => 'aar', 'Aa31LG1G26560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3485' => 'aag', 'Actinidia06854' => 'ach', 'Actinidia12166' => 'ach', 'Actinidia12167' => 'ach', 'Actinidia16266' => 'ach', 'Ah.05g169680' => 'amhyb', 'Ah.05g173400' => 'amhyb', 'Ah.07g199460' => 'amhyb', 'Ah.09g230790' => 'amhyb', 'AL1G63290' => 'aly', 'AL4G44060' => 'aly', 'AL4G44070' => 'aly', 'Aqoxy1G00066' => 'aox', 'Aqoxy1G00276' => 'aox', 'Aqoxy1G00337' => 'aox', 'Aqoxy1G00710' => 'aox', 'Aqoxy5G00229' => 'aox', 'Aqoxy7G00824' => 'aox', 'Aqoxy7G01489' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11HTNE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4D4R47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5G1BL4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60BY7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Q4NXZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J7EN8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNMP4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VCI4LX' => 'arhy', 'AT1G55250' => 'ath', 'AT2G44950' => 'ath', 'AT2G44970' => 'ath', 'ATR0057G002' => 'atr', 'ATR0057G072' => 'atr', 'ATR0598G081' => 'atr', 'ATR0598G355' => 'atr', 'ATR0705G212' => 'atr', 'Atru.chr2.2508' => 'acertr', 'Atru.chr3.2254' => 'acertr', 'Atru.chr5.188' => 'acertr', 'Atru.chr5.189' => 'acertr', 'Atru.chr5.190' => 'acertr', 'Atru.chr5.191' => 'acertr', 'Atru.chr7.1430' => 'acertr', 'Atru.chr7.1431' => 'acertr', 'AUR62004133' => 'cqu', 'AUR62004134' => 'cqu', 'AUR62010927' => 'cqu', 'AUR62013696' => 'cqu', 'AUR62013697' => 'cqu', 'AUR62018970' => 'cqu', 'AUR62021439' => 'cqu', 'AUR62027811' => 'cqu', 'BcaB02g08961' => 'bca', 'BcaB04g16970' => 'bca', 'BcaB06g29409' => 'bca', 'BcaB06g29410' => 'bca', 'BcaC01g01497' => 'bca', 'BcaC02g07125' => 'bca', 'BcaC02g07126' => 'bca', 'BcaC02g12257' => 'bca', 'BcaC05g28641' => 'bca', 'BolC3t21569H' => 'bol', 'BolC4t22223H' => 'bol', 'BolC4t22224H' => 'bol', 'BolC4t28638H' => 'bol', 'BolC4t28639H' => 'bol', 'BolC4t28640H' => 'bol', 'BolC5t33478H' => 'bol', 'BraA04t18819Z' => 'bra', 'BraA04t18820Z' => 'bra', 'BraA05t19481Z' => 'bra', 'BraA05t19482Z' => 'bra', 'BraA08t32135Z' => 'bra', 'C03p92550' => 'bna', 'C04p05920' => 'bna', 'C04p05930' => 'bna', 'C04p71340' => 'bna', 'C04p71350' => 'bna', 'C05p38770' => 'bna', 'C05p47690' => 'bna', 'CAN.G25.2' => 'can', 'CAN.G255.1' => 'can', 'CAN.G899.31' => 'can', 'CANSAT21G1530' => 'cansat', 'CANSAT21G2471' => 'cansat', 'CANSAT56G1115' => 'cansat', 'CANSAT80G2722' => 'cansat', 'CARHR044900' => 'chi', 'CARHR140190' => 'chi', 'CARHR140200' => 'chi', 'Carub.0001s4375' => 'cru', 'Carub.0004s2756' => 'cru', 'Carub.0004s2757' => 'cru', 'Ca_06053_v3' => 'car', 'Ca_07359_v3' => 'car', 'Ca_07362_v3' => 'car', 'Ca_17352_v3' => 'car', 'Ca_23122_v3' => 'car', 'CBR_g45285' => 'cbr', 'Cc01_g01540' => 'ccan', 'Cc02_g24790' => 'ccan', 'Cc02_g24800' => 'ccan', 'Cc06_g10240' => 'ccan', 'Cc06_g10250' => 'ccan', 'CDE02G3843' => 'cde', 'CDE06G2238' => 'cde', 'CDE07G0164' => 'cde', 'CDE07G0948' => 'cde', 'CDE09G0073' => 'cde', 'CDE09G1357' => 'cde', 'CDE09G1392' => 'cde', 'CDE11G0134' => 'cde', 'CDE11G1177' => 'cde', 'Cfa009612' => 'cfa', 'Cfa011114' => 'cfa', 'Cfa011115' => 'cfa', 'Cfa024557' => 'cfa', 'Ciclev10007928m.g' => 'ccl', 'Ciclev10014206m.g' => 'ccl', 'Ciclev10018789m.g' => 'ccl', 'Ciclev10019862m.g' => 'ccl', 'CiPaw.04G159800' => 'cil', 'CiPaw.13G029600' => 'cil', 'CiPaw.13G173000' => 'cil', 'CiPaw.14G023600' => 'cil', 'CiPaw.14G023700' => 'cil', 'ClCG02G023890' => 'cla', 'ClCG05G000330' => 'cla', 'ClCG11G002270' => 'cla', 'COL.COLO4_12450' => 'col', 'COL.COLO4_12451' => 'col', 'COL.COLO4_12521' => 'col', 'COL.COLO4_17533' => 'col', 'COL.COLO4_34783' => 'col', 'COL.COLO4_34990' => 'col', 'Cpa.g.sc101.40' => 'cpa', 'Cpa.g.sc101.41' => 'cpa', 'Cpa.g.sc101.50' => 'cpa', 'Cpa.g.sc119.82' => 'cpa', 'Cpa.g.sc119.83' => 'cpa', 'Cpa.g.sc40.37' => 'cpa', 'Cpa.g.sc40.38' => 'cpa', 'Cre14.g625802' => 'cre', 'CsaV3_2G002030' => 'csa', 'CsaV3_3G007470' => 'csa', 'CsaV3_3G007480' => 'csa', 'CsaV3_4G023460' => 'csa', 'CSS0000015' => 'camsi', 'CSS0010089' => 'camsi', 'CSS0015763' => 'camsi', 'CSS0019024' => 'camsi', 'CSS0026331' => 'camsi', 'DCAR_001994' => 'dca', 'DCAR_012052' => 'dca', 'DCAR_015857' => 'dca', 'DCAR_031362' => 'dca', 'Dinv02630' => 'din', 'Dinv40016' => 'din', 'Dinv44089' => 'din', 'Duzib133G0682' => 'dzi', 'Duzib138G0437' => 'dzi', 'Duzib150G0082' => 'dzi', 'Duzib187G1040' => 'dzi', 'Duzib268G0302' => 'dzi', 'Duzib268G0901' => 'dzi', 'ECA233G3012' => 'eca', 'ECA233G5590' => 'eca', 'ECA234G2180' => 'eca', 'ECA236G0323' => 'eca', 'ECA246G4615' => 'eca', 'EL10Ac1g00804' => 'bvu', 'EL10Ac1g00805' => 'bvu', 'EL10Ac1g01148' => 'bvu', 'EL10Ac8g18409' => 'bvu', 'Eucgr.C01011' => 'egr', 'Eucgr.D02523' => 'egr', 'Eucgr.E02757' => 'egr', 'Eucgr.J01791' => 'egr', 'FAN01G0771' => 'fan', 'FAN01G1926' => 'fan', 'FAN03G0248' => 'fan', 'FAN03G1109' => 'fan', 'FAN03G2712' => 'fan', 'FAN06G2617' => 'fan', 'FAN06G2759' => 'fan', 'FAN06G3263' => 'fan', 'FAN06G3317' => 'fan', 'FAN06G4758' => 'fan', 'FAN10G1201' => 'fan', 'FAN10G2665' => 'fan', 'FAN11G1041' => 'fan', 'FAN16G0771' => 'fan', 'FAN21G1555' => 'fan', 'FAN23G1985' => 'fan', 'FAN25G3163' => 'fan', 'FvH4_1g05810' => 'fve', 'FvH4_3g44811' => 'fve', 'FvH4_7g09500' => 'fve', 'FvH4_7g09510' => 'fve', 'Glyma.01G074000' => 'gma', 'Glyma.02G267300' => 'gma', 'Glyma.03G116900' => 'gma', 'Glyma.07G109900' => 'gma', 'Glyma.11G175700' => 'gma', 'Glyma.14G050200' => 'gma', 'Gohir.A07G007666' => 'ghi', 'Gohir.A07G007732' => 'ghi', 'Gohir.A07G151900' => 'ghi', 'Gohir.A08G029900' => 'ghi', 'Gohir.A08G030000' => 'ghi', 'Gohir.A08G079500' => 'ghi', 'Gohir.A08G137833' => 'ghi', 'Gohir.A11G077100' => 'ghi', 'Gohir.A11G077200' => 'ghi', 'Gohir.D07G008200' => 'ghi', 'Gohir.D08G040700' => 'ghi', 'Gohir.D08G040800' => 'ghi', 'Gohir.D08G089100' => 'ghi', 'Gohir.D08G159100' => 'ghi', 'Gohir.D11G081450' => 'ghi', 'Gohir.D11G081500' => 'ghi', 'Gohir.D11G081600' => 'ghi', 'Gorai.001G008000' => 'gra', 'Gorai.004G039600' => 'gra', 'Gorai.004G039700' => 'gra', 'Gorai.004G093700' => 'gra', 'Gorai.004G165100' => 'gra', 'Gorai.007G087200' => 'gra', 'Gorai.007G087300' => 'gra', 'GSVIVG01015328001' => 'vvi', 'GSVIVG01018220001' => 'vvi', 'GSVIVG01018223001' => 'vvi', 'GSVIVG01025404001' => 'vvi', 'HanXRQChr05g0138451' => 'han', 'HanXRQChr12g0381221' => 'han', 'HanXRQChr13g0404141' => 'han', 'HanXRQChr16g0507631' => 'han', 'HanXRQChr16g0530171' => 'han', 'Haze_02750' => 'cav', 'Haze_02751' => 'cav', 'Haze_02752' => 'cav', 'Haze_22986' => 'cav', 'Hma1.2p1_0086F.1_g044970' => 'hma', 'Hma1.2p1_0341F.1_g130550' => 'hma', 'Hma1.2p1_0945F.1_g240270' => 'hma', 'Hma1.2p1_0972F.1_g242820' => 'hma', 'HPP92_003454' => 'vpl', 'HPP92_007991' => 'vpl', 'HPP92_015119' => 'vpl', 'Hund09237' => 'sun', 'Hund17071' => 'sun', 'Hund17072' => 'sun', 'Hund26987' => 'sun', 'Hund27392' => 'sun', 'Hund27393' => 'sun', 'Lalb_Chr03g0040151' => 'lal', 'Lalb_Chr04g0250131' => 'lal', 'Lalb_Chr04g0250141' => 'lal', 'Lalb_Chr12g0210621' => 'lal', 'Lalb_Chr16g0388031' => 'lal', 'Lalb_Chr17g0347201' => 'lal', 'Lalb_Chr19g0126661' => 'lal', 'Lj1g0014311' => 'lja', 'Lj2C713G1' => 'lonja', 'Lj3g0026230' => 'lja', 'Lj4g0020736' => 'lja', 'Lj7A661G50' => 'lonja', 'Lj9A560G41' => 'lonja', 'Lj9C561T4' => 'lonja', 'LjContig00029g0005450' => 'lja', 'Lsat_1_v5_gn_4_112920' => 'lsa', 'Lsat_1_v5_gn_4_25980' => 'lsa', 'Lsat_1_v5_gn_4_43721' => 'lsa', 'Lsat_1_v5_gn_5_26140' => 'lsa', 'Lsat_1_v5_gn_6_52501' => 'lsa', 'Lsat_1_v5_gn_7_11360' => 'lsa', 'Lsat_1_v5_gn_8_97241' => 'lsa', 'Manes.01G271200' => 'mes', 'Manes.05G051800' => 'mes', 'Manes.05G051900' => 'mes', 'Manes.15G105500' => 'mes', 'Manes.16G111100' => 'mes', 'Mapoly0035s0133' => 'mpo', 'Mapoly0163s0016' => 'mpo', 'MBI04_g09530_MAGBIO' => 'mbi', 'MBI04_g09531_MAGBIO' => 'mbi', 'MBI04_g27062_MAGBIO' => 'mbi', 'MBI13_g29634_MAGBIO' => 'mbi', 'MBI14_g40985_MAGBIO' => 'mbi', 'MCO10G245' => 'mco', 'MCO10G346' => 'mco', 'MD02G1060100' => 'mdo', 'MD02G1218200' => 'mdo', 'MD02G1218300' => 'mdo', 'MD07G1098600' => 'mdo', 'MD07G1098900' => 'mdo', 'MD08G1204500' => 'mdo', 'MD08G1205100' => 'mdo', 'MD15G1388900' => 'mdo', 'MD15G1389000' => 'mdo', 'Medtr1g068830' => 'mtr', 'Medtr3g060950' => 'mtr', 'Medtr5g065540' => 'mtr', 'Medtr5g085010' => 'mtr', 'Medtr7g046250' => 'mtr', 'Medtr8g006370' => 'mtr', 'Medtr8g064230' => 'mtr', 'Medtr8g102820' => 'mtr', 'MELO3C004578.2' => 'cme', 'MELO3C005969.2' => 'cme', 'MELO3C005971.2' => 'cme', 'MELO3C014670.2' => 'cme', 'Migut.B01559' => 'egut', 'Migut.B01560' => 'egut', 'Migut.D02533' => 'egut', 'Migut.J01114' => 'egut', 'Migut.K00521' => 'egut', 'MSTRG.17144' => 'ama', 'MSTRG.20952' => 'ama', 'Nitab4.5_0000012g0230' => 'nta', 'Nitab4.5_0000051g0250' => 'nta', 'Nitab4.5_0000775g0150' => 'nta', 'Nitab4.5_0003110g0110' => 'nta', 'Nitab4.5_0003199g0050' => 'nta', 'Nitab4.5_0004415g0030' => 'nta', 'Nitab4.5_0009626g0010' => 'nta', 'Nitab4.5_0011368g0020' => 'nta', 'Nn1g00928' => 'nnu', 'Nn1g00929' => 'nnu', 'Nn3g18171' => 'nnu', 'Nn3g20644' => 'nnu', 'Nn7g35936' => 'nnu', 'Oeu000047.1' => 'oeu', 'Oeu029373.1' => 'oeu', 'Oeu051908.1' => 'oeu', 'Oeu061501.1' => 'oeu', 'Oeu061502.1' => 'oeu', 'Oeu063219.1' => 'oeu', 'Oeu064896.1' => 'oeu', 'Os04g0550400' => 'osa', 'Os05g0557900' => 'osa', 'Os10g0565600' => 'osa', 'Os11g0110000' => 'osa', 'Os12g0110100' => 'osa', 'Peaxi162Scf00001g00912' => 'pax', 'Peaxi162Scf00001g05810' => 'pax', 'Peaxi162Scf00018g00310' => 'pax', 'Peaxi162Scf00018g00311' => 'pax', 'Peaxi162Scf00100g00714' => 'pax', 'Peaxi162Scf00100g00715' => 'pax', 'Peaxi162Scf00377g00828' => 'pax', 'PGR004G1697' => 'pgr', 'PGR004G1996' => 'pgr', 'PGR044G1558' => 'pgr', 'PGR142G3510' => 'pgr', 'PGSC0003DMG400025982' => 'stu', 'PGSC0003DMG400027433' => 'stu', 'Phvul.008G141100' => 'pvu', 'Phvul.008G214800' => 'pvu', 'Phvul.010G054100' => 'pvu', 'Potri.001G008800' => 'ptr', 'Potri.002G141300' => 'ptr', 'Potri.003G216651' => 'ptr', 'Potri.014G055800' => 'ptr', 'Potri.014G055900' => 'ptr', 'Potri.018G085600' => 'ptr', 'Pp3c10_17220' => 'ppa', 'Pp3c10_17225' => 'ppa', 'Pp3c12_18130' => 'ppa', 'Pp3c13_8530' => 'ppa', 'Pp3c16_2030' => 'ppa', 'Pp3c19_17420' => 'ppa', 'Pp3c25_1490' => 'ppa', 'Pp3c5_12440' => 'ppa', 'Pp3c6_18000' => 'ppa', 'PRCOL_00000945' => 'pco', 'Prupe.1G536900' => 'ppe', 'Prupe.1G537100' => 'ppe', 'Prupe.2G122700' => 'ppe', 'Prupe.2G122900' => 'ppe', 'Prupe.7G222800' => 'ppe', 'Psat2g026520' => 'psa', 'Psat3g180600' => 'psa', 'Psat4g226960' => 'psa', 'PSO017G0984' => 'pso', 'PSO063G7067' => 'pso', 'PSO170G3933' => 'pso', 'PSO339G1017' => 'pso', 'PSO384G2650' => 'pso', 'PSO566G0058' => 'pso', 'PSO782G0434' => 'pso', 'PSO782G1681' => 'pso', 'QL01p007971' => 'qlo', 'QL02p042390' => 'qlo', 'QL02p042393' => 'qlo', 'QL04p034731' => 'qlo', 'QL04p034746' => 'qlo', 'RcHm_v2.0_Chr1g0346301' => 'rch', 'RcHm_v2.0_Chr1g0346311' => 'rch', 'RcHm_v2.0_Chr2g0091461' => 'rch', 'RcHm_v2.0_Chr5g0081511' => 'rch', 'Rhsim01G0185500' => 'rsi', 'Rhsim07G0033300' => 'rsi', 'Rhsim07G0033400' => 'rsi', 'Sabra01G0006800' => 'sbr', 'Sabra02G0110200' => 'sbr', 'Sabra14G0041000' => 'sbr', 'Sabra14G0041100' => 'sbr', 'Sabra18G0073900' => 'sbr', 'SalBow5G0694' => 'sbo', 'SalBow5G0872' => 'sbo', 'SalBow5G3422' => 'sbo', 'Sc01g0000800' => 'sci', 'Sc02g0002930' => 'sci', 'Sc08g0007830' => 'sci', 'Sc25g0000760' => 'sci', 'Sed0002705' => 'sed', 'Sed0005356' => 'sed', 'Sed0017278' => 'sed', 'Sed0019139' => 'sed', 'SEGI_05355' => 'sgi', 'SEGI_07034' => 'sgi', 'SEGI_15435' => 'sgi', 'SEGI_31179' => 'sgi', 'SGA_v2.0_scaffold129G34159' => 'sas', 'SGA_v2.0_scaffold153G36926' => 'sas', 'SGA_v2.0_scaffold153G36928' => 'sas', 'SGA_v2.0_scaffold153G36935' => 'sas', 'SGA_v2.0_scaffold311G48240' => 'sas', 'SGA_v2.0_scaffold52G19205' => 'sas', 'SGA_v2.0_scaffold6G03439' => 'sas', 'SHI13592' => 'shi', 'SHI13593' => 'shi', 'SHI13594' => 'shi', 'SHI13595' => 'shi', 'SHI31263' => 'shi', 'SMO165G0146' => 'smo', 'SMO174G0047' => 'smo', 'Solyc01g006040.3' => 'sly', 'Solyc01g090590.3' => 'sly', 'Solyc05g016715.1' => 'sly', 'Solyc05g018210.3' => 'sly', 'Solyc11g013370.3' => 'sly', 'Sopen01g002040' => 'spe', 'Sopen01g036340' => 'spe', 'Sopen02g016010' => 'spe', 'Sopen04g022610' => 'spe', 'Sopen05g014950' => 'spe', 'Sopen11g008390' => 'spe', 'Sp1g40910' => 'spa', 'Sp4g27030' => 'spa', 'Sp4g27040' => 'spa', 'TAR374G1704' => 'tar', 'TAR375G0817' => 'tar', 'TAR383G0989' => 'tar', 'TAR503G0002' => 'tar', 'TAR626G1913' => 'tar', 'TAR633G0029' => 'tar', 'TAR633G1852' => 'tar', 'THA.LOC104815657' => 'tha', 'THA.LOC104817201' => 'tha', 'THA.LOC104817202' => 'tha', 'Thecc.01G387900' => 'tca', 'Thecc.01G388000' => 'tca', 'Thecc.09G103600' => 'tca', 'Thecc.09G213500' => 'tca', 'Thhalv10001306m.g' => 'esa', 'Thhalv10001413m.g' => 'esa', 'Thhalv10011229m.g' => 'esa', 'TPR.G23498' => 'tpr', 'TPR.G25640' => 'tpr', 'TPR.G28932' => 'tpr', 'TPR.G39045' => 'tpr', 'TWI23G0115' => 'twi', 'TWI23G0632' => 'twi', 'TWI32G0195' => 'twi', 'TWI32G0864' => 'twi', 'TWI34G1236' => 'twi', 'TWI59G0329' => 'twi', 'unitig_22.g5401' => 'ugi', 'unitig_22.g5848' => 'ugi', 'unitig_8.g3840' => 'ugi', 'vmacro03817' => 'vma', 'vmacro03818' => 'vma', 'vmacro06241' => 'vma', 'vmacro13472' => 'vma', 'vmacro13473' => 'vma', 'VMungo0331G0080' => 'vmu', 'VMungo0647G1617' => 'vmu', 'VMungo1383G0153' => 'vmu', 'Zm00001eb019800' => 'zma', 'Zm00001eb163330' => 'zma', 'Zm00001eb224300' => 'zma', 'Zm00001eb226640' => 'zma', 'Zm00001eb273100' => 'zma', 'Zm00001eb295510' => 'zma' ) $gf_id = 'HOM05D001240' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001240' ) $data_identifier = 'HOM05D001240' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 7, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 6, 'cpa' => (int) 7, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 9, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 7, 'shi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb295510' $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